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Source code for galaxy.datatypes.converters.interval_to_interval_index_converter

#!/usr/bin/env python

Convert from interval file to interval index file.

usage: %prog <options> in_file out_file
    -c, --chr-col: chromosome column, default=1
    -s, --start-col: start column, default=2
    -e, --end-col: end column, default=3

import optparse

from bx.interval_index_file import Indexes

[docs]def main(): # Read options, args. parser = optparse.OptionParser() parser.add_option("-c", "--chr-col", type="int", dest="chrom_col", default=1) parser.add_option("-s", "--start-col", type="int", dest="start_col", default=2) parser.add_option("-e", "--end-col", type="int", dest="end_col", default=3) (options, args) = parser.parse_args() input_fname, output_fname = args # Make column indices 0-based. options.chrom_col -= 1 options.start_col -= 1 options.end_col -= 1 # Do conversion. index = Indexes() offset = 0 with open(input_fname) as in_fh: for line in in_fh: feature = line.strip().split() if not feature or feature[0].startswith("track") or feature[0].startswith("#"): offset += len(line) continue chrom = feature[options.chrom_col] chrom_start = int(feature[options.start_col]) chrom_end = int(feature[options.end_col]) index.add(chrom, chrom_start, chrom_end, offset) offset += len(line) with open(output_fname, "wb") as out: index.write(out)
if __name__ == "__main__": main()